Rice (Oryza sativa L.) is an excellent model plant in elucidation of cereal domestication. Loss of seed shattering, weakened dormancy, and changes in plant architecture were thought to be three key events in the rice domestication and creating the high-yield, uniform-germinating, and densely-planting modern rice. Loss of shattering is considered to be the direct morphological evidence for identifying domesticated rice. Two major shattering QTLs, Sh4 and qSH1, have displayed different domestication histories. Weakened seed dormancy is essential for synchronous germination in agricultural production. Genes Sdr4, qSD7-1, and qSD12 impose a global and complementary adaptation strategies in controlling seed dormancy. The prostrate growth habit of wild rice is an adaptation to disturbed habitats, while the erect growth habit of rice cultivars meet the needs of compact planting, and such a plant architecture is mainly controlled by PROG1. The outcrossing habit of wild rice promotes propagation of domestication genes among dif-ferent populations, while the self-pollinating habit of cultivated rice facilitates fixation of domestication genes. Currently, the researches on rice domestication mainly focus on individual genes or multiple neutral markers, and much less attention has been paid to the evolution of network controlling domestication traits. With the progress in functional genomics re-search, the molecular mechanism of domestication traits is emerging. Rice domestication researches based on network will be more comprehensive and better reflect rice domestication process. Here, we reviewed most progresses in molecular mechanisms of rice domestication traits, in order to provide the new insights for rice domestication and molecular breeding.
[1] Wasylikowa K, Dahlberg J. Sorghum in the economy of the Early Neolithic Nomadic Tribes at Nabta Playa, Southern Egypt. In: Van der Veen M, ed. The exploitation of plant resources in ancient Africa. New York: Kluwer/ Plenum, 1999: 11-32.
[2] Darwin C. The variation of animals and plants under domestication. Cambridge: Cambridge University Press, 2010.
[3] Harlan JR. Crops & man. Madison, Wis: American Society of Agronomy, 1975.
[4] Hammer K. Das Domestikationssyndrom. Genet Resour Crop Evol, 1984, 32(1): 11-34.
[5] Harlan JR. Crops & man (2nd ed). Madison, Wis: American Society of Agronomy, 1992.
[6] Sweeney M, McCouch S. The complex history of the domestication of rice. Ann Bot, 2007, 100(5): 951-957.
[7] Vaughan DA, Lu BR, Tomooka N. Was asian rice (Oryza sativa) domesticated more than once? Rice, 2008, 1(1): 16-24.
[8] Vaughan DA, Morishima H, Kadowaki K. Diversity in the Oryza genus. Curr Opin Plant Biol, 2003, 6(2): 139-146.
[9] Project IRGS. The map-based sequence of the rice genome. Nature, 2005, 436(7052): 793-800.
[10] Ouyang S, Zhu W, Hamilton J, Lin HN, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR. The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res, 2007, 35(Database issue): D883-D887.
[11] Li YN, Uhm T, Ren CW, Wu CC, Santos TS, Lee MK, Yan B, Santos F, Zhang AM, Scheuring C, Sanchez A, Millena AC, Nguyen HT, Kou HD, Liu DQ, Zhang HB. A plant- transformation-competent BIBAC/BAC-based map of rice for functional analysis and genetic engineering of its genomic sequence. Genome, 2007, 50(3): 278-288.
[12] Molina J, Sikora M, Garud N, Flowers JM, Rubinstein S, Reynolds A, Huang P, Jackson S, Schaal BA, Bustamante CD, Boyko AR, Purugganan MD. Molecular evidence for a single evolutionary origin of domesticated rice. Proc Natl Acad Sci USA, 2011, 108(20): 8351-8356.
[13] Xu X, Liu X, Ge S, Jensen JD, Hu FY, Li X, Dong Y, Gutenkunst RN, Fang L, Huang L, Li JX, He WM, Zhang GJ, Zheng XM, Zhang FM, Li YR, Yu C, Kristiansen K, Zhang XQ, Wang J, Wright M, McCouch S, Nielsen R, Wang J, Wang W. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol, 2011, 30(1): 105-111.
[14] Li CB, Zhou AL, Sang T. Rice domestication by reducing shattering. Science, 2006, 311(5769): 1936-1939.
[15] Zhang LB, Zhu QH, Wu ZQ, Ross-Ibarra J, Gaut BS, Ge S, Sang T. Selection on grain shattering genes and rates of rice domestication. New Phytol, 2009, 184(3): 708-720.
[16] He ZW, Zhai WW, Wen HJ, Tang T, Wang Y, Lu XM, Greenberg AJ, Hudson RR, Wu CI, Shi SH. Two evolutionary histories in the genome of rice: the roles of domestication genes. PLoS Genet, 2011, 7(6): e1002100.
[17] Kovach MJ, Sweeney MT, McCouch SR. New insights into the history of rice domestication. Trends Genet, 2007, 23(11): 578-587.
[18] 姜恭好, 徐才国, 李香花, 何予卿. 利用双单倍体群体剖析水稻产量及其相关性状的遗传基础. 遗传学报, 2004, 31(1): 63-72.
[19] Onishi K, Horiuchi Y, Ishigoh-Oka N, Takagi K, Ichikawa N, Maruoka M, Sano Y. A QTL cluster for plant architecture and its ecological significance in asian wild rice. Breed Sci, 2007, 57(1): 7-16.
[20] Jiang YH, Cai ZX, Xie WB, Long T, Yu HH, Zhang QF. Rice functional genomics research: Progress and implications for crop genetic improvement. Biotechnol Adv, 2012, 30(5): 1059-1070.
[21] Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T, Yano M. An SNP caused loss of seed shattering during rice domestication. Science, 2006, 312(5778): 1392-1396.
[22] Gu XY, Liu T, Feng J, Suttle JC, Gibbons J. The qSD12 underlying gene promotes abscisic acid accumulation in early developing seeds to induce primary dormancy in rice. Plant Mol Biol
